Chicken Chromosome Linkages

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Chicken Chromosome Linkage Map Table

The following linkage map table was based on the following books:

  • 1. Crawford (ed.) (1990) Poultry Breeding and Genetics. Elsevier, Amsterdam.
  • 2. Stevens, L. (1991) Genetics and Evolution of the Domestic Fowl. Cambridge University Press, Cambridge [England].
  • 3. Muir and Aggrey (ed.) (2003) Poultry Genetics, Breeding and Biotechnology. CABI Publishing.

Additional data was gathered from many scientific journal papers, all of which are cited in the reference section.

Chromosome 1

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
O Blue Egg-Shell SLCO1B3 Wang et al. 2013. [34] , Wragg et al. 2013. [36]
cha Charcoal
P Pea comb SOX5 (SRY-box 5) Wright et al. 2009.[1] Sato et al. 2010.[2]
Db Dark Brown SOX10 (SRY-box 10) Gunnarsson et al. 2011.[3]
Ml Melanotic Ml is 45 + map units from P
Pg Pattern
no close linkage to above
c (cre, ca) Recessive White TYR (Tyrosinase) Chang et al, 2006.[4] Sato et. al, 2007.[5]

Chromosome 2

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
DV, DC Duplex Comb EOMES (Eomesodermin) Dorshorst et al 2010.[6]

Dorshorst et al 2015.[40]

M Multiple Spurs
Po, PoD Polydactyly, Duplicate Lmbr1 (limb region 1) Chromosome 2 - Dorshorst et al 2010.[6]

Might be SHH (Sonic HedgeHog) instead of Lmbr1. Dunn et al., 2011.[7]

Zhang et al 2016. [42] Further evidence there are 2 different Po genes (Chinese breeds & Sultans different sequence to European breeds Houdan, Dorkings & Faverolles), He et al 2017.[47]

no close linkage to above
Rp Rumpless Irx1 and Irx2 (Iroquois homeobox) Rooksana et al, 2012.[8]

Chromosome 3

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Ea-P Blood Group P * new to 3, due to linkage with Na
Na Naked Neck BMP12/GDF7 (bone morphogenetic protein 12)(growth differentiation factor 7) Pitel et al. 2000.[9] Mou et al. 2011.[10]
h Hookless - Silkiness PDSS2 Feng et al 2014. [39] Dorshorst et al 2010.[6]
Fl Flightless possible Chromosome 3. Due to close linkage with h - hookless

Chromosome 4

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
mo, mo^w Mottled, White EDNRB2

(Endothelin Receptor B2)

Kinoshita et al. 2014.[38]
no known linkage to above
sc Scaleless FGF20

(Fibroblast growth factor 20)

Wells et al. 2012.[33]

Chromosome 6

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
ig Inhibitor of Gold (Cream) COMTD1

(catechol-O-methyltransferase domain containing 1)

Eriksson, 2012.[11]

Chromosome 7

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Cp Creeper IHH (Indian hedgehog) Jin et al. 2016.[45]
R Rose comb MNR2 (homeodomain protein)

(& CCDC108 coiled-coil domain containing 108 )

Imsland et al. 2012.[12]
U Uropygial linkage not given to lav.
the below not linear
lav 32.5 Lavender MLPH (melanophilin) lav 32.5 map units to R.

Vaez et al., 2008.[13]

 ? linkage not given between lav & Mp
Mp 16 Mp 16 map units to R
the above not linear end of linkage group 1
Ade-B adenine synthesis B Ade-B in linkage group VIII

Chromosome 8

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
FMO3 Fishy taint (eggs & meat) FMO3 (flavincontaining

mono-oxygenase 3)

Honkatukia et al. 2005.[14]

Hamid et al. 2012.[15]

Chromosome 10

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Hf Henny feathering CYP19A1 (cytochrome P450, family 19, subfamily A, polypeptide 1) ref: OMIA

Microchromosome 11

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
E E, ER, ER- Fay, eWh, e+, eb, es, ebc, ey (E series) MC1R

(melanocortin-1 receptor)

Takeuchi et al. 1996.[16], Kerje et al. 2003.[17]

Ling et al. 2003.[18]

E & mo loci 26 cM linkage proposed by Brumbaugh & Hollander, 1965. [19]

Further study indicated that this E-mo 26 cM relationship was not repeatable. Ref. Smyth & Ponce de Leon, 1992. [43]

mo (EDNRB2) locus found on Chromosome 4 in 2014. Ref. Kinoshita et al. 2014.[38]

Microchromosome 12

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Bl Blue MITF *possible candidate - not sequenced in chickens.

Minvielle et al. 2010.[20]

no known linkage to above
lo Congenital loco Okumura et al. 2013.[37]

Microchromosome 13

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Pti Feathered legs Chromosome 13 -

Dorshorst et al. 2010.[6]

Microchromosome 15

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Et Ear Tuft TBX1, partial GNB1L

(T-box 1)

Rooksana et al, 2012.[8]

Microchromosome 16 (17)

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
R-Rs 1
NOR Nucleolar organiser region

Microchromosome 20

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Fm Fibromelanosis EDN3 (Endothelin 3) Chromosome 20 - Dorshorst et al. 2010.[6]
  • might be EDN3 - not substantiated

Dorshorst et al. 2011.[21], Shinomiya et al. 2011.[22]

Microchromosome 24

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
w Yellow Skin BCDO2 (beta-carotene dioxygenase 2) Eriksson et al. 2008.[23]
Ea-H Blood Group H

Microchromosome 25

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
 ? Beak Deformity LOC426217 (claw keratin-like) Bai et al. 2016.[41]

Microchromosome 27

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
Mb Muff beard HOXB8 (Homeobox B8) Guo et al. 2016.[44]

Microchromosome 33 (Linkage Group E22C19W28)

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
fr Fray
Cr Crest HOXC8

(Homeobox protein C8)

Wang et al. 2012.[24]
I, ID, IS Dominant White, Dun, Smoky PMEL17

(Melanocyte protein Pmel 17)

Kerje et al. 2004.[25]
F Frizzle KRT75


Ng et al. 2012.[26]

Z Chromosome: sex-linked

Locus Map Unit Locus Description Scientific Name Comments/ Ref.
ro Restricted Ovulator
sh Shaker
n Naked
px Paroxysm
ln Liver Necrosis
dwB, dwM, dw Dwarf GHR (growth hormone receptor) Hull et al. 1999.[27]
wl Wingless
pn Prenatal Lethal
ev21 Endogenous viral 21 EV21 (ALVE21)

(Endogenous viral 21)

Tixier-Boichard et al. 1997.[28],

Bacon et al. 1988.[29]

Kn, Ks, K Slow Feathering / Late Feathering PRLR and SPEF2

(prolactin receptor)(sperm flagellar 2)

Elferink et al. 2008.[30]
S, Sal-s, sal Silver, Imperfect Albinism SLC45A2

(solute carrier family 45 member 2)

Gunnarsson et al, 2007.[31]
lk Lady Killer
Li Light Down
y Recessive White Skin or WHAM (Wisconsin hypoalpha mutant) ABCA1 (ATP-binding cassette, sub-family A (ABC1), member 1) Attie et al. 2002. [35]
br Brown Eye
Id, ida, idc,idM Dermal Melanin Inhibitor VCAN (Versican) or B4GALT1 (beta1,4-Galactosyltransferase) Might be VCAN or B4GALT1 - not substantiated.

Dorshorst et al. 2010.[6]

BSd, B Sex-linked Dilution, Barring CDKN2A/B

(Cyclin-dependent kinas inhibitor 2A/B)

Hellström et al. 2010.[32] ,

Schwochow Thalmann et al. 2017.[46]

ko Head Streak


Ref. No. Year Reference Paper URL
1 2009 Wright D, Boije H, Meadows JRS, Bed'hom B, Gourichon D, et al. (2009) Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens. PLoS Genet 5(6): e1000512. doi:10.1371/journal.pgen.1000512. [Full]
2 2010 Sato S, Otake T, Suzuki C, Uemoto Y, Saburi J, Hashimoto H, Kobayashi E. (2010) Sequence analysis of a pea comb locus on chicken chromosome 1. Animal Genetics. Volume 41, Issue 6, pages 659–661, December 2010. [Abstract]
3 2011 Gunnarsson U, Kerje S, Bed'hom B, Sahlqvist AS, Ekwall O, Tixier-Boichard M, Kämpe O, Andersson L. (2011) The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res. 2011 Apr;24(2):268-74. doi: 10.1111/j.1755-148X.2011.00825.x. Epub 2011 Jan 25. [Abstract]
4 2006 Chang C, Coville JL, Coquerelle G, Gourichon D, Oulmouden A, and Tixier-Boichard M. (2006) Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics. 2006; 7: 19. [Full]
5 2007 Sato S, Otake T, Suzuki C, Saburi J, Kobayashi E. (2007) Mapping of the recessive white locus and analysis of the tyrosinase gene in chickens. Poult Sci. 2007 Oct;86(10):2126-33. [Full]
6 2010 Dorshorst B, Okimoto R, Ashwell C. (2010) Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken. J Hered. 2010 May-Jun;101(3):339-50 [Full]
7 2011 Dunn IC, Paton IR, Clelland AK, Sebastian S, Johnson EJ, McTeir L, Windsor D, Sherman A, Sang H, Burt DW, Tickle C, Davey MG. (2011) The chicken polydactyly (Po) locus causes allelic imbalance and ectopic expression of Shh during limb development. Dev Dyn. 2011 May;240(5):1163-72. doi: 10.1002/dvdy.22623. Epub 2011 Apr 4. [Full]
8 2012 Rooksana E. Noorai, Nowlan H. Freese, Lindsay M. Wright, Susan C. Chapman, and Leigh Anne Clark. (2012) Genome-Wide Association Mapping and Identification of Candidate Genes for the Rumpless and Ear-tufted Traits of the Araucana Chicken. PLoS One. 2012; 7(7): e40974. [Full]
9 2000 Pitel F, Berge R, Coquerelle G, Crooijmans RPMA, Groenen MAM, et al. (2000) Mapping the naked neck (NA) and polydactyly (PO) mutants of the chicken with microsatellite molecular markers. Genet Sel Evol 32: 73–86. [Full]
10 2011 Mou C, Pitel F, Gourichon D, Vignoles F, Tzika A, et al. (2011) Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering. PLoS Biol 9(3): e1001028. doi:10.1371/journal.pbio.1001028 [Full]
11 2012 Eriksson, J (2012) Genetic and Genomic Studies in Chicken: Assigning Function to Vertebrate Genes. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 732. 55pp. Uppsala. ISBN 978-91-554-8246-6. [Full]
12 2012 Imsland F, Feng C, Boije H, Bed'hom B, Fillon V, Dorshorst B, Rubin CJ, Liu R, Gao Y, Gu X, Wang Y, Gourichon D, Zody MC, Zecchin W, Vieaud A, Tixier-Boichard M, Hu X, Hallböök F, Li N, Andersson L.(2012) The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility. PLoS Genet. 2012 Jun;8(6):e1002775. Epub 2012 Jun 28. [Full]
13 2008 Vaez M, Follett SA, Bed'hom B, Gourichon D, Tixier-Boichard M, Burke T. (2008) A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken. BMC Genet. 2008 Jan 15;9:7. doi: 10.1186/1471-2156-9-7. [Full]
14 2005 Honkatukia M, Reese K, Preisinger R, Tuiskula-Haavisto M, Weigend S, Roito J, Mäki-Tanila A, Vilkki J. (2005) Fishy taint in chicken eggs is associated with a substitution within a conserved motif of the FMO3 gene. Genomics. 2005 Aug;86(2):225-32. [Full]
15 2012 Hamid MA, Wang X, and Zhao X. (2012) Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mismatch amplification mutation assay (MAMA-PCR) in chickens. African Journal of Biotechnology Vol. 11(7), pp. 1823-1828, 24 January, 2012 [Full]
16 1996 Takeuchi S, Suzuki H, Yabuuchi M and Takahashi S. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the chicken. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression Volume 1308, Issue 2, 14 August 1996, Pages 164-168. [Abstract]
17 2003 Kerje S, Lind J, Schütz K, Jensen P, Andersson L. (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet. 2003 Aug;34(4):241-8. [Abstract]
18 2003 Ling MK, Lagerström MC, Fredriksson R, Okimoto R, Mundy NI, Takeuchi S, Schiöth HB. (2003) Association of feather colour with constitutively active melanocortin 1 receptors in chicken. Eur J Biochem. 2003 Apr;270(7):1441-9. [Full]
19 1965 Brumbaugh, J. A., and W. F. Hollander (1965) A further study of the E pattern locus in the fowl. Iowa State J. of Science, 40; 51-64 No online paper.
20 2010 Minvielle F, Bed'hom B, Coville JL, Ito S, Inoue-Murayama M, Gourichon D. (2010) The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with the "blue" chicken plumage. BMC Genet. 2010 Feb 25;11:15. doi: 10.1186/1471-2156-11-15. [Full]
21 2011 Dorshorst B, Molin AM, Rubin CJ, Johansson AM, Strömstedt L, Pham MH, Chen CF, Hallböök F, Ashwell C, Andersson L. (2011) A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. 2011 Dec;7(12):e1002412. Epub 2011 Dec 22. [Full]
22 2011 Shinomiya A, Kayashima Y, Kinoshita K, Mizutani M, Namikawa T, Matsuda Y, Akiyama T. (2011) Gene Duplication of endothelin 3 is Closely Correlated with the Hyperpigmentation of the Internal Organs (Fibromelanosis) in Silky Chickens. Genetics. 2012 Feb;190(2):627-38. doi: 10.1534/genetics.111.136705. Epub 2011 Nov 30. [Full]
23 2008 Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, et al. (2008) Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genet 4(2): e1000010. doi:10.1371/journal.pgen.1000010. [Full]
24 2012 Wang Y, Gao Y, Imsland F, Gu X, Feng C, et al. (2012) The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin. PLoS ONE 7(4): e34012. doi:10.1371/journal.pone.0034012. [Abstract]
25 2004 Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schütz K, Jensen P, von Heijne G, Okimoto R, Andersson L. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics. 2004 Nov;168(3):1507-18. [Full]
26 2012 Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH, Chuong CM. (2012) The Chicken Frizzle Feather Is Due to an a-Keratin (KRT75) Mutation That Causes a Defective Rachis. PLoS Genet. 2012 Jul;8(7):e1002748. Epub 2012 Jul 19. [Full]
27 1999 Hull, K.L, Marsh, J.A. and Harvey, S. (1999) A missense mutation in the GHR gene of Cornell sex-linked dwarf chickens does not abolish serum GH binding. Journal of Endocrinology (1999) 161, 495–50. [Full]
28 1997 Tixier-Boichard M, Boulliou-Robic A, Morisson M, Coquerelle G, Horst P, Benkel B. (1997) A deleted retroviral insertion at the ev21-K complex locus in Indonesian chickens. Poult Sci. 1997 May;76(5):733-42 [Full]
29 1988 Bacon LD, Smith E, Crittenden LB, Havenstein GB. (1988) Association of the slow feathering (K) and an endogenous viral (ev21) gene on the Z chromosome of chickens. Poult Sci. 1988 Feb;67(2):191-7 [Abstract]
30 2008 Elferink MG, Vallée AA, Jungerius AP, Crooijmans RP, Groenen MA. (2008) Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics. 2008 Aug 20;9:391. [Full]
31 2007 Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed'hom B, Ito S, Jensen P, Rattink A, Vereijken A, Andersson L. (2007). Mutations in SLC45A2 Cause Plumage Color Variation in Chicken and Japanese Quail. Genetics. 175, 867-77. [Full]
32 2010 Hellström AR, Sundström E, Gunnarsson U, Bed'Hom B, Tixier-Boichard M, Honaker CF, Sahlqvist AS, Jensen P, Kämpe O, Siegel PB, Kerje S, Andersson L. (2010) Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus. Pigment Cell Melanoma Res. 2010 Aug;23(4):521-30. doi: 10.1111/j.1755-148X.2010.00700.x. Epub 2010 Mar 29. [Full]
33 2012 Wells KL, Hadad Y, Ben-Avraham D, Hillel J, Cahaner A and Heado DJ. (2012) Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens. BMC Genomics 2012, 13:257 doi:10.1186/1471-2164-13-257. [Full]
34 2013 Wang Z, Qu L, Yao J, Yang X, Li G, Zhang Y, Li J, Wang X, Bai J, Xu G, Deng X, Yang N, Wu C. (2013) An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken. PLoS Genet. 2013 January; 9(1): e1003183. [Full]
35 2002 Attie, A. D., Hamon, Y., Brooks-Wilson, A.R., Gray-Keller, M.P., MacDonald, M.L.E., Rigot, V., Tebon, A., Zhang, L., Mulligan, J.D., Singaraja, R.R., Bitgood, J.J., Cook M.E., Kastelein, J.J.P., Chimini, G. and Hayden, M. R. (2002) Identification and functional analysis of a naturally occurring E89K mutation in the ABCA1 gene of the WHAM chicken. The Journal of Lipid Research, October 2002. 43, 1610-1617. [Full]
36 2013 Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han J-L, Gongora J, Gourichon D, Tixier-Boichard M, Hanotte O. (2013) Endogenous Retrovirus EAV-HP Linked to Blue Egg Phenotype in Mapuche Fowl. PLoS ONE 8(8): e71393. doi:10.1371/journal.pone.0071393 [Full]
37 2013 Okumura, Y., Ohtake, T., Uemoto, Y., Sato, S., Sato, S. and Kobayashi, E. (2013) Fine mapping of the chicken congenital loco locus on chromosome 12. Animal Genetics. doi: 10.1111/age.12065 [Abstract]
38 2014 Kinoshita K, Akiyama T, Mizutani M, Shinomiya A, Ishikawa A, et al. (2014) Endothelin Receptor B2 (EDNRB2) Is Responsible for the Tyrosinase-Independent Recessive White (mow) and Mottled (mo) Plumage Phenotypes in the Chicken. PLoS ONE 9(1): e86361. doi:10.1371/journal.pone.0086361 [Full]
39 2014 Feng, C., Gao, Y., Dorshorst, B., Song, C., Gu, X., Li, Q., Li, N. et al. (2014) A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens. PLoS Genetics, 10(8), e1004576. doi:10.1371/journal.pgen.1004576 [Full]
40 2015 Dorshorst B, Harun-Or-Rashid M, Bagherpoor A.J, Rubin C, Ashwell C, Gourichon D, Tixier-Boichard M, Hallböök F, Andersson L. (2015) A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes. PLoS Genet. 2015 March; 11(3): e1004947. [Full]
41 2016 Bai, H., Sun, Y., Zhu, J., Liu, N., Li, D., Xue, F., … Chen, J. (2016) Study on LOC426217 as a candidate gene for beak deformity in chicken. BMC Genetics, 17, 44. [Full]
42 2016 Zhang, Z., Nie, C., Jia, Y., Jiang, R., Xia, H., Lv, X., … Qu, L. (2016) Parallel Evolution of Polydactyly Traits in Chinese and European Chickens. PLoS ONE, 11(2), e0149010. [Full]
43 1992 Smyth, R., Ponce de Leon, F.A. (1992) Research Note: Linkage Relationship Between the Pea Comb (P) and Extended Black (E) Loci of the Chicken. Poultry Science (1992) 71 (1): 208-210. [Full]
44 2016 Guo Y, Gu X, Sheng Z, et al. (2016) A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens. Leeb T, ed. PLoS Genetics. 2016;12(6):e1006071. doi:10.1371/journal.pgen.1006071. [Full]
45 2016 Jin, S., Zhu, F., Wang, Y., Yi, G., Li, J., Lian, L., … Yang, N. (2016). Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken. Scientific Reports, 2016, 6, 30172. [Full]
46 2017 Schwochow Thalmann, D., Ring, H., Sundström, E., Cao, X., Larsson, M., Kerje, S., … Andersson, L. (2017). The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A. PLoS Genetics, 13(4), e1006665. [Full]
47 2017 He, C., Chen, Y., Yang, K., Zhai, Z., Zhao, W., Liu, S., … Meng, H. (2017). Genetic pattern and gene localization of polydactyly in Beijing fatty chicken. PLoS ONE, 12(5), e0176113. [Full]
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